Starting phenix.real_space_refine on Tue May 20 07:06:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyq_34376/05_2025/8gyq_34376.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 12726 2.51 5 N 3402 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "G" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.52, per 1000 atoms: 0.58 Number of scatterers: 19712 At special positions: 0 Unit cell: (125.19, 125.19, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3493 8.00 N 3402 7.00 C 12726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 86 " " NAG B 701 " - " ASN B 86 " " NAG C 701 " - " ASN C 86 " " NAG D 701 " - " ASN D 86 " " NAG E 701 " - " ASN E 86 " " NAG F 701 " - " ASN F 86 " " NAG G 701 " - " ASN G 86 " Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 75.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.815A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.767A pdb=" N TRP A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 183 removed outlier: 4.011A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.291A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 5.472A pdb=" N THR A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix removed outlier: 4.004A pdb=" N GLU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.827A pdb=" N ARG A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix removed outlier: 3.759A pdb=" N THR A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 314 removed outlier: 3.624A pdb=" N GLY A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.589A pdb=" N TRP A 336 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.675A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.897A pdb=" N ASN A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.262A pdb=" N ASP A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.699A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.502A pdb=" N ARG B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.900A pdb=" N TRP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 183 removed outlier: 3.932A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.404A pdb=" N LEU B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 5.691A pdb=" N THR B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.023A pdb=" N GLU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.928A pdb=" N ARG B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.871A pdb=" N VAL B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 283 through 314 Processing helix chain 'B' and resid 319 through 329 removed outlier: 3.911A pdb=" N VAL B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.615A pdb=" N TRP B 336 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.634A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.919A pdb=" N ASN B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.891A pdb=" N ASP B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.976A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 76 removed outlier: 3.862A pdb=" N ARG C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.943A pdb=" N TRP C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 183 removed outlier: 3.998A pdb=" N LYS C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Proline residue: C 125 - end of helix removed outlier: 4.349A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 5.666A pdb=" N THR C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Proline residue: C 174 - end of helix removed outlier: 4.048A pdb=" N GLU C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 283 through 314 removed outlier: 3.523A pdb=" N GLY C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.752A pdb=" N VAL C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.929A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.916A pdb=" N ASN C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.725A pdb=" N ASP C 376 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.710A pdb=" N ALA C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 76 removed outlier: 3.789A pdb=" N ARG D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Proline residue: D 62 - end of helix Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.888A pdb=" N TRP D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 183 removed outlier: 3.992A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 4.316A pdb=" N LEU D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 5.734A pdb=" N THR D 148 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix removed outlier: 4.059A pdb=" N GLU D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 251 removed outlier: 3.848A pdb=" N VAL D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Proline residue: D 241 - end of helix removed outlier: 3.784A pdb=" N THR D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 314 removed outlier: 3.572A pdb=" N GLY D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.762A pdb=" N VAL D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.563A pdb=" N TRP D 336 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.907A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.801A pdb=" N ASN D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 removed outlier: 4.019A pdb=" N ASP D 376 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.717A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 removed outlier: 5.107A pdb=" N VAL E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.812A pdb=" N TRP E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 183 removed outlier: 4.001A pdb=" N LYS E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Proline residue: E 125 - end of helix removed outlier: 4.308A pdb=" N LEU E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 5.663A pdb=" N THR E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Proline residue: E 174 - end of helix removed outlier: 4.030A pdb=" N GLU E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 202 Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 251 removed outlier: 3.842A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Proline residue: E 241 - end of helix removed outlier: 3.566A pdb=" N THR E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 314 removed outlier: 3.602A pdb=" N GLY E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.767A pdb=" N VAL E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.582A pdb=" N TRP E 336 " --> pdb=" O ARG E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 3.864A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 358 through 367 removed outlier: 3.888A pdb=" N ASN E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 366 " --> pdb=" O ASN E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.954A pdb=" N ASP E 376 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.730A pdb=" N ALA E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 removed outlier: 5.112A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Proline residue: F 62 - end of helix Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.828A pdb=" N TRP F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 183 removed outlier: 4.028A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Proline residue: F 125 - end of helix removed outlier: 4.377A pdb=" N LEU F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Proline residue: F 138 - end of helix removed outlier: 5.491A pdb=" N THR F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Proline residue: F 174 - end of helix removed outlier: 4.015A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 204 through 219 removed outlier: 3.816A pdb=" N ARG F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 251 removed outlier: 3.843A pdb=" N VAL F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Proline residue: F 241 - end of helix removed outlier: 3.746A pdb=" N THR F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 314 removed outlier: 3.641A pdb=" N GLY F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.590A pdb=" N TRP F 336 " --> pdb=" O ARG F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.794A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 358 through 367 removed outlier: 4.045A pdb=" N ASN F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 376 removed outlier: 4.190A pdb=" N ASP F 376 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.682A pdb=" N ALA F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 76 removed outlier: 5.109A pdb=" N VAL G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) Proline residue: G 62 - end of helix Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.810A pdb=" N TRP G 100 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 183 removed outlier: 3.964A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 4.283A pdb=" N LEU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Proline residue: G 138 - end of helix removed outlier: 5.496A pdb=" N THR G 148 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Proline residue: G 174 - end of helix removed outlier: 4.001A pdb=" N GLU G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'G' and resid 204 through 219 removed outlier: 3.846A pdb=" N ARG G 219 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 251 removed outlier: 3.854A pdb=" N VAL G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Proline residue: G 241 - end of helix Processing helix chain 'G' and resid 283 through 314 removed outlier: 3.578A pdb=" N GLY G 292 " --> pdb=" O ARG G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 removed outlier: 3.784A pdb=" N VAL G 328 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 removed outlier: 3.594A pdb=" N TRP G 336 " --> pdb=" O ARG G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.990A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 358 through 367 removed outlier: 3.958A pdb=" N ASN G 362 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 363 " --> pdb=" O LYS G 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 366 " --> pdb=" O ASN G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 376 removed outlier: 4.260A pdb=" N ASP G 376 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.691A pdb=" N ALA G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 1244 hydrogen bonds defined for protein. 3669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6310 1.34 - 1.46: 2516 1.46 - 1.57: 11186 1.57 - 1.69: 1 1.69 - 1.81: 119 Bond restraints: 20132 Sorted by residual: bond pdb=" CG PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.48e+00 bond pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.10e+00 bond pdb=" N LEU D 48 " pdb=" CA LEU D 48 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.41e-02 5.03e+03 5.00e+00 bond pdb=" CB PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" C PRO A 49 " pdb=" O PRO A 49 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.30e-02 5.92e+03 1.69e+00 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26746 1.79 - 3.58: 456 3.58 - 5.37: 60 5.37 - 7.16: 4 7.16 - 8.95: 6 Bond angle restraints: 27272 Sorted by residual: angle pdb=" CA PRO C 49 " pdb=" N PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.59e+01 angle pdb=" N PRO C 49 " pdb=" CD PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 103.20 96.31 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" CB LYS A 203 " pdb=" CG LYS A 203 " pdb=" CD LYS A 203 " ideal model delta sigma weight residual 111.30 120.25 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CB LYS F 203 " pdb=" CG LYS F 203 " pdb=" CD LYS F 203 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" CB LYS C 203 " pdb=" CG LYS C 203 " pdb=" CD LYS C 203 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10459 17.93 - 35.87: 1345 35.87 - 53.80: 430 53.80 - 71.73: 57 71.73 - 89.67: 22 Dihedral angle restraints: 12313 sinusoidal: 5138 harmonic: 7175 Sorted by residual: dihedral pdb=" CA VAL A 378 " pdb=" C VAL A 378 " pdb=" N VAL A 379 " pdb=" CA VAL A 379 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL G 378 " pdb=" C VAL G 378 " pdb=" N VAL G 379 " pdb=" CA VAL G 379 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA VAL D 378 " pdb=" C VAL D 378 " pdb=" N VAL D 379 " pdb=" CA VAL D 379 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2228 0.033 - 0.067: 660 0.067 - 0.100: 174 0.100 - 0.133: 58 0.133 - 0.167: 2 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA LEU A 48 " pdb=" N LEU A 48 " pdb=" C LEU A 48 " pdb=" CB LEU A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA LEU D 48 " pdb=" N LEU D 48 " pdb=" C LEU D 48 " pdb=" CB LEU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA PRO B 49 " pdb=" N PRO B 49 " pdb=" C PRO B 49 " pdb=" CB PRO B 49 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 3119 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " -0.167 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" CG ASN C 86 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.565 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 86 " -0.189 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" CG ASN B 86 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 86 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 86 " 0.374 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 86 " 0.083 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN G 86 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN G 86 " 0.074 2.00e-02 2.50e+03 pdb=" ND2 ASN G 86 " -0.289 2.00e-02 2.50e+03 pdb=" C1 NAG G 701 " 0.176 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 114 2.45 - 3.06: 14039 3.06 - 3.68: 30523 3.68 - 4.29: 41389 4.29 - 4.90: 69771 Nonbonded interactions: 155836 Sorted by model distance: nonbonded pdb=" OD2 ASP C 51 " pdb=" OH TYR C 227 " model vdw 1.840 3.040 nonbonded pdb=" OG1 THR D 88 " pdb=" OD1 ASP D 90 " model vdw 1.903 3.040 nonbonded pdb=" OD2 ASP A 51 " pdb=" OH TYR A 227 " model vdw 1.914 3.040 nonbonded pdb=" OG1 THR B 88 " pdb=" OD1 ASP B 90 " model vdw 1.956 3.040 nonbonded pdb=" OD2 ASP F 51 " pdb=" OH TYR F 227 " model vdw 2.003 3.040 ... (remaining 155831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 41.670 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20153 Z= 0.145 Angle : 0.779 54.732 27321 Z= 0.351 Chirality : 0.035 0.167 3122 Planarity : 0.005 0.149 3458 Dihedral : 17.626 89.668 7595 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.56 % Rotamer: Outliers : 0.66 % Allowed : 26.32 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2394 helix: 1.49 (0.13), residues: 1540 sheet: -1.76 (0.60), residues: 105 loop : -2.51 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.002 0.000 HIS D 357 PHE 0.019 0.001 PHE A 50 TYR 0.013 0.001 TYR B 249 ARG 0.005 0.000 ARG D 167 Details of bonding type rmsd link_NAG-ASN : bond 0.06834 ( 7) link_NAG-ASN : angle 18.76226 ( 21) hydrogen bonds : bond 0.10313 ( 1244) hydrogen bonds : angle 5.46858 ( 3669) SS BOND : bond 0.00247 ( 14) SS BOND : angle 0.42481 ( 28) covalent geometry : bond 0.00293 (20132) covalent geometry : angle 0.58089 (27272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 HIS cc_start: 0.8494 (t70) cc_final: 0.7908 (t-170) REVERT: A 380 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7103 (mtt180) REVERT: C 160 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: C 342 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7970 (p) REVERT: D 326 HIS cc_start: 0.8307 (t70) cc_final: 0.7924 (t70) REVERT: D 342 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8149 (p) REVERT: D 350 PHE cc_start: 0.7413 (m-80) cc_final: 0.7158 (m-80) REVERT: E 160 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5686 (tt0) REVERT: E 326 HIS cc_start: 0.8445 (t70) cc_final: 0.8064 (t-170) REVERT: E 342 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7516 (p) REVERT: F 160 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5471 (tt0) REVERT: G 160 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5309 (tt0) REVERT: G 326 HIS cc_start: 0.8651 (t70) cc_final: 0.8034 (t-170) REVERT: G 342 CYS cc_start: 0.8394 (t) cc_final: 0.7833 (p) REVERT: G 380 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6954 (mtt90) outliers start: 14 outliers final: 4 residues processed: 270 average time/residue: 0.2697 time to fit residues: 117.3839 Evaluate side-chains 240 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 0.0020 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 319 ASN B 163 ASN B 254 GLN B 326 HIS C 121 HIS C 319 ASN D 252 GLN D 254 GLN D 357 HIS F 207 GLN F 319 ASN G 254 GLN G 319 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.197541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130502 restraints weight = 27083.911| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.97 r_work: 0.3577 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20153 Z= 0.149 Angle : 0.692 17.347 27321 Z= 0.335 Chirality : 0.044 0.702 3122 Planarity : 0.005 0.094 3458 Dihedral : 7.176 77.409 2830 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.56 % Allowed : 24.20 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2394 helix: 1.46 (0.13), residues: 1603 sheet: -1.66 (0.60), residues: 105 loop : -2.55 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 115 HIS 0.003 0.000 HIS D 357 PHE 0.024 0.001 PHE A 350 TYR 0.013 0.001 TYR A 165 ARG 0.013 0.000 ARG E 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 7) link_NAG-ASN : angle 7.74974 ( 21) hydrogen bonds : bond 0.03693 ( 1244) hydrogen bonds : angle 4.41035 ( 3669) SS BOND : bond 0.00363 ( 14) SS BOND : angle 0.52400 ( 28) covalent geometry : bond 0.00345 (20132) covalent geometry : angle 0.65781 (27272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 249 time to evaluate : 2.063 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6900 (tp) cc_final: 0.6653 (tp) REVERT: A 160 GLU cc_start: 0.4431 (OUTLIER) cc_final: 0.3729 (tt0) REVERT: A 210 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: A 326 HIS cc_start: 0.8267 (t70) cc_final: 0.7719 (t-170) REVERT: B 51 ASP cc_start: 0.7202 (m-30) cc_final: 0.6978 (m-30) REVERT: B 252 GLN cc_start: 0.8160 (tp40) cc_final: 0.7817 (tp40) REVERT: C 135 MET cc_start: 0.8797 (tpp) cc_final: 0.8549 (mmm) REVERT: C 160 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.5113 (tt0) REVERT: C 210 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: D 210 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: D 326 HIS cc_start: 0.7989 (t70) cc_final: 0.7716 (t70) REVERT: D 350 PHE cc_start: 0.7598 (m-80) cc_final: 0.7120 (m-80) REVERT: E 160 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4859 (tt0) REVERT: E 207 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: E 210 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: E 326 HIS cc_start: 0.8216 (t70) cc_final: 0.7841 (t-170) REVERT: F 160 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4321 (tt0) REVERT: F 210 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6007 (m-80) REVERT: G 160 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.4644 (tt0) REVERT: G 326 HIS cc_start: 0.8397 (t70) cc_final: 0.7859 (t-170) REVERT: G 342 CYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7828 (p) outliers start: 97 outliers final: 52 residues processed: 309 average time/residue: 0.2720 time to fit residues: 135.1032 Evaluate side-chains 274 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 377 ASN C 319 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.190439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124264 restraints weight = 27142.851| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.78 r_work: 0.3528 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 20153 Z= 0.212 Angle : 0.703 15.715 27321 Z= 0.343 Chirality : 0.044 0.645 3122 Planarity : 0.005 0.075 3458 Dihedral : 6.990 72.145 2819 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.91 % Allowed : 24.15 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2394 helix: 1.35 (0.13), residues: 1631 sheet: -1.75 (0.59), residues: 105 loop : -2.57 (0.27), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 115 HIS 0.005 0.001 HIS B 326 PHE 0.021 0.002 PHE C 50 TYR 0.016 0.002 TYR B 213 ARG 0.006 0.000 ARG F 104 Details of bonding type rmsd link_NAG-ASN : bond 0.01028 ( 7) link_NAG-ASN : angle 7.03663 ( 21) hydrogen bonds : bond 0.03910 ( 1244) hydrogen bonds : angle 4.44567 ( 3669) SS BOND : bond 0.00715 ( 14) SS BOND : angle 0.62036 ( 28) covalent geometry : bond 0.00522 (20132) covalent geometry : angle 0.67611 (27272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 220 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.3887 (tt0) REVERT: A 210 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: A 326 HIS cc_start: 0.8404 (t70) cc_final: 0.7857 (t-170) REVERT: B 51 ASP cc_start: 0.7598 (m-30) cc_final: 0.7319 (m-30) REVERT: B 191 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: B 254 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: B 334 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7238 (ttp80) REVERT: B 377 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6670 (m-40) REVERT: C 160 GLU cc_start: 0.5308 (OUTLIER) cc_final: 0.4930 (tt0) REVERT: C 210 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: D 210 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: D 350 PHE cc_start: 0.7636 (m-80) cc_final: 0.7219 (m-80) REVERT: E 160 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.4962 (tt0) REVERT: E 210 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: E 326 HIS cc_start: 0.8292 (t70) cc_final: 0.7894 (t-170) REVERT: F 160 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4355 (tt0) REVERT: F 210 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: F 380 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7390 (mtt90) REVERT: G 42 LEU cc_start: 0.1018 (OUTLIER) cc_final: 0.0747 (pp) REVERT: G 160 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4407 (tt0) REVERT: G 210 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: G 326 HIS cc_start: 0.8413 (t70) cc_final: 0.7895 (t-170) REVERT: G 342 CYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8013 (p) REVERT: G 350 PHE cc_start: 0.7561 (m-80) cc_final: 0.7256 (m-80) outliers start: 147 outliers final: 110 residues processed: 325 average time/residue: 0.2615 time to fit residues: 137.5004 Evaluate side-chains 329 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 203 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 103 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 235 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 chunk 209 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 163 ASN B 198 ASN B 326 HIS C 362 ASN D 91 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 121 HIS F 319 ASN F 362 ASN F 377 ASN G 255 ASN G 319 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.198288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130521 restraints weight = 27180.714| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.04 r_work: 0.3588 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20153 Z= 0.123 Angle : 0.625 13.566 27321 Z= 0.306 Chirality : 0.041 0.526 3122 Planarity : 0.005 0.069 3458 Dihedral : 6.476 68.339 2819 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.84 % Allowed : 26.50 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2394 helix: 1.67 (0.13), residues: 1638 sheet: -1.42 (0.58), residues: 105 loop : -2.52 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.006 0.000 HIS B 326 PHE 0.028 0.001 PHE F 350 TYR 0.016 0.001 TYR B 249 ARG 0.008 0.000 ARG B 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 7) link_NAG-ASN : angle 5.88280 ( 21) hydrogen bonds : bond 0.03306 ( 1244) hydrogen bonds : angle 4.15441 ( 3669) SS BOND : bond 0.00161 ( 14) SS BOND : angle 0.66872 ( 28) covalent geometry : bond 0.00263 (20132) covalent geometry : angle 0.60393 (27272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 234 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4291 (OUTLIER) cc_final: 0.3611 (tt0) REVERT: A 210 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6036 (m-80) REVERT: A 326 HIS cc_start: 0.8278 (t70) cc_final: 0.8042 (t70) REVERT: A 380 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7330 (mtm180) REVERT: B 51 ASP cc_start: 0.7492 (m-30) cc_final: 0.7259 (m-30) REVERT: C 191 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 210 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: C 309 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7086 (mp) REVERT: D 210 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: D 350 PHE cc_start: 0.7533 (m-80) cc_final: 0.7060 (m-80) REVERT: D 357 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.5863 (m-70) REVERT: E 160 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.4791 (tt0) REVERT: E 210 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: E 326 HIS cc_start: 0.8138 (t70) cc_final: 0.7756 (t-170) REVERT: F 150 LEU cc_start: 0.6909 (tp) cc_final: 0.6664 (tp) REVERT: F 160 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.4420 (tt0) REVERT: F 210 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: F 380 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7520 (mtt90) REVERT: G 42 LEU cc_start: 0.1061 (OUTLIER) cc_final: 0.0795 (pp) REVERT: G 160 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4195 (tt0) REVERT: G 210 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: G 326 HIS cc_start: 0.8292 (t70) cc_final: 0.7833 (t-170) REVERT: G 342 CYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7791 (p) REVERT: G 350 PHE cc_start: 0.7527 (m-80) cc_final: 0.7311 (m-80) REVERT: G 380 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7589 (mtm180) outliers start: 103 outliers final: 60 residues processed: 309 average time/residue: 0.2602 time to fit residues: 129.9581 Evaluate side-chains 274 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 200 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 156 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 326 HIS ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.194108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125427 restraints weight = 27404.271| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.01 r_work: 0.3522 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20153 Z= 0.174 Angle : 0.654 16.144 27321 Z= 0.322 Chirality : 0.042 0.524 3122 Planarity : 0.005 0.071 3458 Dihedral : 6.312 59.782 2816 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.30 % Allowed : 25.94 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2394 helix: 1.59 (0.13), residues: 1645 sheet: -1.60 (0.56), residues: 105 loop : -2.62 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 115 HIS 0.004 0.001 HIS B 326 PHE 0.019 0.001 PHE C 156 TYR 0.016 0.002 TYR B 213 ARG 0.005 0.000 ARG B 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 7) link_NAG-ASN : angle 6.45193 ( 21) hydrogen bonds : bond 0.03617 ( 1244) hydrogen bonds : angle 4.26518 ( 3669) SS BOND : bond 0.00551 ( 14) SS BOND : angle 0.57621 ( 28) covalent geometry : bond 0.00426 (20132) covalent geometry : angle 0.62980 (27272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 211 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4456 (OUTLIER) cc_final: 0.3791 (tt0) REVERT: A 210 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: A 326 HIS cc_start: 0.8382 (t70) cc_final: 0.8160 (t70) REVERT: B 51 ASP cc_start: 0.7698 (m-30) cc_final: 0.7376 (m-30) REVERT: B 135 MET cc_start: 0.8165 (mmp) cc_final: 0.7834 (mmt) REVERT: B 334 ARG cc_start: 0.7592 (ptp90) cc_final: 0.7325 (ttp80) REVERT: C 191 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 135 MET cc_start: 0.8833 (tpp) cc_final: 0.8544 (mmm) REVERT: D 210 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6828 (m-80) REVERT: D 350 PHE cc_start: 0.7615 (m-80) cc_final: 0.7174 (m-80) REVERT: D 357 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5947 (m-70) REVERT: E 160 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.4854 (tt0) REVERT: E 210 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: E 326 HIS cc_start: 0.8219 (t70) cc_final: 0.7857 (t-170) REVERT: F 160 GLU cc_start: 0.5242 (OUTLIER) cc_final: 0.4462 (tt0) REVERT: F 210 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: F 380 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7721 (mtt90) REVERT: G 42 LEU cc_start: 0.1085 (OUTLIER) cc_final: 0.0851 (pp) REVERT: G 160 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4365 (tt0) REVERT: G 210 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: G 326 HIS cc_start: 0.8366 (t70) cc_final: 0.7990 (t-170) REVERT: G 342 CYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7905 (p) REVERT: G 380 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7272 (mtm180) outliers start: 134 outliers final: 93 residues processed: 305 average time/residue: 0.2648 time to fit residues: 130.0819 Evaluate side-chains 305 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 200 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 158 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 287 GLN B 362 ASN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.195960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127654 restraints weight = 27022.155| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.02 r_work: 0.3557 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20153 Z= 0.133 Angle : 0.630 14.220 27321 Z= 0.309 Chirality : 0.041 0.500 3122 Planarity : 0.005 0.066 3458 Dihedral : 6.048 57.980 2816 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.92 % Allowed : 26.55 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2394 helix: 1.68 (0.13), residues: 1652 sheet: -1.36 (0.56), residues: 105 loop : -2.59 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.002 0.000 HIS F 311 PHE 0.017 0.001 PHE A 350 TYR 0.014 0.001 TYR B 213 ARG 0.010 0.000 ARG C 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 7) link_NAG-ASN : angle 5.93784 ( 21) hydrogen bonds : bond 0.03342 ( 1244) hydrogen bonds : angle 4.15135 ( 3669) SS BOND : bond 0.00319 ( 14) SS BOND : angle 0.57101 ( 28) covalent geometry : bond 0.00305 (20132) covalent geometry : angle 0.60832 (27272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 230 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4411 (OUTLIER) cc_final: 0.3758 (tt0) REVERT: A 210 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6011 (m-80) REVERT: A 326 HIS cc_start: 0.8360 (t70) cc_final: 0.8135 (t70) REVERT: A 332 THR cc_start: 0.4818 (OUTLIER) cc_final: 0.4519 (p) REVERT: B 51 ASP cc_start: 0.7669 (m-30) cc_final: 0.7362 (m-30) REVERT: B 135 MET cc_start: 0.8493 (mmp) cc_final: 0.8262 (mmt) REVERT: B 197 GLU cc_start: 0.9022 (mm-30) cc_final: 0.7999 (pp20) REVERT: B 198 ASN cc_start: 0.8239 (t0) cc_final: 0.7898 (t0) REVERT: B 334 ARG cc_start: 0.7592 (ptp90) cc_final: 0.7320 (ttp80) REVERT: B 359 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6174 (mppt) REVERT: C 380 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6346 (mtm-85) REVERT: D 135 MET cc_start: 0.8827 (tpp) cc_final: 0.8568 (mmm) REVERT: D 210 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: D 350 PHE cc_start: 0.7559 (m-80) cc_final: 0.7131 (m-80) REVERT: D 357 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5910 (m-70) REVERT: E 160 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4661 (tt0) REVERT: E 210 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: E 326 HIS cc_start: 0.8189 (t70) cc_final: 0.7825 (t-170) REVERT: F 160 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4435 (tt0) REVERT: F 210 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: F 380 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7765 (mtt90) REVERT: G 42 LEU cc_start: 0.1059 (OUTLIER) cc_final: 0.0834 (pp) REVERT: G 160 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4320 (tt0) REVERT: G 210 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: G 326 HIS cc_start: 0.8366 (t70) cc_final: 0.8020 (t-170) REVERT: G 380 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7175 (mtm180) outliers start: 126 outliers final: 86 residues processed: 325 average time/residue: 0.2779 time to fit residues: 142.8504 Evaluate side-chains 303 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 204 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 39 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 287 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.195930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129198 restraints weight = 26966.842| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.63 r_work: 0.3523 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20153 Z= 0.127 Angle : 0.625 13.707 27321 Z= 0.307 Chirality : 0.040 0.491 3122 Planarity : 0.005 0.069 3458 Dihedral : 5.935 58.479 2816 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.64 % Allowed : 27.49 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2394 helix: 1.81 (0.13), residues: 1631 sheet: -1.23 (0.57), residues: 105 loop : -2.53 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.002 0.000 HIS F 311 PHE 0.030 0.001 PHE F 350 TYR 0.023 0.001 TYR B 136 ARG 0.007 0.000 ARG B 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 7) link_NAG-ASN : angle 5.75529 ( 21) hydrogen bonds : bond 0.03271 ( 1244) hydrogen bonds : angle 4.11911 ( 3669) SS BOND : bond 0.00295 ( 14) SS BOND : angle 0.53111 ( 28) covalent geometry : bond 0.00292 (20132) covalent geometry : angle 0.60505 (27272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 224 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.3902 (tt0) REVERT: A 210 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6009 (m-80) REVERT: A 326 HIS cc_start: 0.8289 (t70) cc_final: 0.8070 (t70) REVERT: A 332 THR cc_start: 0.4858 (OUTLIER) cc_final: 0.4567 (p) REVERT: B 51 ASP cc_start: 0.7625 (m-30) cc_final: 0.7333 (m-30) REVERT: B 190 ARG cc_start: 0.7706 (tmm160) cc_final: 0.6379 (mtm180) REVERT: B 197 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8051 (pp20) REVERT: B 198 ASN cc_start: 0.8248 (t0) cc_final: 0.7877 (t0) REVERT: B 334 ARG cc_start: 0.7595 (ptp90) cc_final: 0.7282 (ttp80) REVERT: B 359 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.6023 (mppt) REVERT: C 191 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 135 MET cc_start: 0.8796 (tpp) cc_final: 0.8572 (mmm) REVERT: D 210 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: D 350 PHE cc_start: 0.7512 (m-80) cc_final: 0.7065 (m-80) REVERT: D 357 HIS cc_start: 0.6179 (m-70) cc_final: 0.5883 (m-70) REVERT: E 160 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4598 (tt0) REVERT: E 210 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: E 326 HIS cc_start: 0.8129 (t70) cc_final: 0.7769 (t-170) REVERT: E 342 CYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7554 (p) REVERT: E 380 ARG cc_start: 0.6878 (mtt180) cc_final: 0.6543 (mtm-85) REVERT: F 160 GLU cc_start: 0.5062 (OUTLIER) cc_final: 0.4319 (tt0) REVERT: F 210 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: F 380 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7740 (mtt90) REVERT: G 42 LEU cc_start: 0.1107 (OUTLIER) cc_final: 0.0865 (pp) REVERT: G 160 GLU cc_start: 0.4867 (OUTLIER) cc_final: 0.4227 (tt0) REVERT: G 210 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: G 326 HIS cc_start: 0.8286 (t70) cc_final: 0.7948 (t-170) outliers start: 120 outliers final: 82 residues processed: 315 average time/residue: 0.2645 time to fit residues: 133.6399 Evaluate side-chains 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 209 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain E residue 375 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 177 optimal weight: 0.0050 chunk 121 optimal weight: 0.2980 chunk 113 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 201 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 287 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.196295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131085 restraints weight = 27264.737| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.78 r_work: 0.3511 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20153 Z= 0.132 Angle : 0.631 13.136 27321 Z= 0.309 Chirality : 0.041 0.483 3122 Planarity : 0.005 0.065 3458 Dihedral : 5.875 59.572 2816 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.03 % Allowed : 28.05 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2394 helix: 1.81 (0.13), residues: 1638 sheet: -1.08 (0.57), residues: 105 loop : -2.56 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.003 0.000 HIS A 311 PHE 0.045 0.001 PHE E 350 TYR 0.017 0.001 TYR B 136 ARG 0.007 0.000 ARG C 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 7) link_NAG-ASN : angle 5.36772 ( 21) hydrogen bonds : bond 0.03271 ( 1244) hydrogen bonds : angle 4.12568 ( 3669) SS BOND : bond 0.00320 ( 14) SS BOND : angle 0.51947 ( 28) covalent geometry : bond 0.00305 (20132) covalent geometry : angle 0.61323 (27272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 227 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.4015 (tt0) REVERT: A 210 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: A 326 HIS cc_start: 0.8299 (t70) cc_final: 0.8078 (t70) REVERT: A 332 THR cc_start: 0.4975 (OUTLIER) cc_final: 0.4693 (p) REVERT: B 51 ASP cc_start: 0.7662 (m-30) cc_final: 0.7369 (m-30) REVERT: B 190 ARG cc_start: 0.7906 (tmm160) cc_final: 0.6603 (mtm180) REVERT: B 197 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8098 (pp20) REVERT: B 198 ASN cc_start: 0.8241 (t0) cc_final: 0.7852 (t0) REVERT: B 334 ARG cc_start: 0.7604 (ptp90) cc_final: 0.7300 (ttp80) REVERT: B 359 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6198 (mppt) REVERT: C 191 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 342 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7764 (p) REVERT: D 135 MET cc_start: 0.8783 (tpp) cc_final: 0.8563 (mmm) REVERT: D 210 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: D 350 PHE cc_start: 0.7518 (m-80) cc_final: 0.7086 (m-80) REVERT: D 357 HIS cc_start: 0.6285 (m-70) cc_final: 0.5949 (m-70) REVERT: E 160 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.4789 (tt0) REVERT: E 210 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: E 326 HIS cc_start: 0.8159 (t70) cc_final: 0.7787 (t-170) REVERT: E 342 CYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7596 (p) REVERT: E 380 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6638 (mtm-85) REVERT: F 160 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4350 (tt0) REVERT: F 210 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: F 326 HIS cc_start: 0.8126 (t70) cc_final: 0.7788 (t-170) REVERT: F 380 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7796 (mtt90) REVERT: G 42 LEU cc_start: 0.1030 (OUTLIER) cc_final: 0.0791 (pp) REVERT: G 160 GLU cc_start: 0.4853 (OUTLIER) cc_final: 0.4159 (tt0) REVERT: G 210 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: G 326 HIS cc_start: 0.8290 (t70) cc_final: 0.7985 (t-170) REVERT: G 342 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7971 (p) outliers start: 107 outliers final: 83 residues processed: 305 average time/residue: 0.2825 time to fit residues: 137.5942 Evaluate side-chains 308 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 210 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 180 optimal weight: 6.9990 chunk 109 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 225 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 198 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.198020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130103 restraints weight = 26962.007| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.06 r_work: 0.3591 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20153 Z= 0.118 Angle : 0.629 12.477 27321 Z= 0.308 Chirality : 0.041 0.536 3122 Planarity : 0.005 0.061 3458 Dihedral : 5.716 58.403 2816 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.18 % Allowed : 28.85 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2394 helix: 1.96 (0.13), residues: 1631 sheet: -0.84 (0.59), residues: 105 loop : -2.54 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.003 0.000 HIS A 311 PHE 0.045 0.001 PHE E 350 TYR 0.015 0.001 TYR B 136 ARG 0.007 0.000 ARG D 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 7) link_NAG-ASN : angle 5.21226 ( 21) hydrogen bonds : bond 0.03115 ( 1244) hydrogen bonds : angle 4.05437 ( 3669) SS BOND : bond 0.00196 ( 14) SS BOND : angle 0.55699 ( 28) covalent geometry : bond 0.00259 (20132) covalent geometry : angle 0.61283 (27272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 234 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8025 (mmp) cc_final: 0.7149 (mmt) REVERT: A 160 GLU cc_start: 0.4449 (OUTLIER) cc_final: 0.3942 (tt0) REVERT: A 210 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: A 326 HIS cc_start: 0.8292 (t70) cc_final: 0.8066 (t70) REVERT: A 332 THR cc_start: 0.5102 (OUTLIER) cc_final: 0.4825 (p) REVERT: B 51 ASP cc_start: 0.7591 (m-30) cc_final: 0.7340 (m-30) REVERT: B 190 ARG cc_start: 0.7949 (tmm160) cc_final: 0.6623 (mtm180) REVERT: B 197 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8040 (pp20) REVERT: B 198 ASN cc_start: 0.8238 (t0) cc_final: 0.7793 (t0) REVERT: B 334 ARG cc_start: 0.7611 (ptp90) cc_final: 0.7342 (ttp80) REVERT: B 359 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.6021 (mppt) REVERT: C 191 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 266 ASP cc_start: 0.6510 (m-30) cc_final: 0.6206 (m-30) REVERT: C 342 CYS cc_start: 0.8730 (t) cc_final: 0.7731 (p) REVERT: C 380 ARG cc_start: 0.6861 (mtt90) cc_final: 0.6418 (mtm180) REVERT: D 210 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: D 342 CYS cc_start: 0.8617 (t) cc_final: 0.7931 (p) REVERT: D 350 PHE cc_start: 0.7513 (m-80) cc_final: 0.7167 (m-80) REVERT: D 357 HIS cc_start: 0.6104 (m-70) cc_final: 0.5794 (m-70) REVERT: E 160 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.4878 (tt0) REVERT: E 210 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: E 326 HIS cc_start: 0.8235 (t70) cc_final: 0.8010 (t-170) REVERT: E 342 CYS cc_start: 0.8561 (t) cc_final: 0.7579 (p) REVERT: E 380 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6811 (mtm-85) REVERT: F 160 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4508 (tt0) REVERT: F 210 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6135 (m-80) REVERT: F 326 HIS cc_start: 0.8189 (t70) cc_final: 0.7838 (t-170) REVERT: F 380 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7800 (mtt90) REVERT: G 42 LEU cc_start: 0.1116 (OUTLIER) cc_final: 0.0876 (pp) REVERT: G 136 TYR cc_start: 0.8203 (t80) cc_final: 0.7959 (t80) REVERT: G 160 GLU cc_start: 0.5106 (OUTLIER) cc_final: 0.4462 (tt0) REVERT: G 210 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: G 326 HIS cc_start: 0.8345 (t70) cc_final: 0.8022 (t-170) REVERT: G 342 CYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7852 (p) outliers start: 89 outliers final: 67 residues processed: 301 average time/residue: 0.2828 time to fit residues: 133.9080 Evaluate side-chains 299 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 217 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.195457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.127834 restraints weight = 26962.545| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.98 r_work: 0.3552 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20153 Z= 0.154 Angle : 0.653 12.115 27321 Z= 0.322 Chirality : 0.042 0.532 3122 Planarity : 0.005 0.063 3458 Dihedral : 5.735 59.442 2816 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.37 % Allowed : 28.99 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2394 helix: 1.83 (0.13), residues: 1638 sheet: -0.91 (0.58), residues: 105 loop : -2.54 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 115 HIS 0.003 0.000 HIS A 311 PHE 0.043 0.001 PHE E 350 TYR 0.021 0.001 TYR B 213 ARG 0.009 0.000 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00870 ( 7) link_NAG-ASN : angle 5.16166 ( 21) hydrogen bonds : bond 0.03356 ( 1244) hydrogen bonds : angle 4.15815 ( 3669) SS BOND : bond 0.00413 ( 14) SS BOND : angle 0.51985 ( 28) covalent geometry : bond 0.00366 (20132) covalent geometry : angle 0.63722 (27272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 221 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8214 (mmp) cc_final: 0.8004 (mmp) REVERT: A 160 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.4120 (tt0) REVERT: A 210 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: A 326 HIS cc_start: 0.8392 (t70) cc_final: 0.8164 (t70) REVERT: A 332 THR cc_start: 0.5149 (OUTLIER) cc_final: 0.4844 (p) REVERT: B 51 ASP cc_start: 0.7753 (m-30) cc_final: 0.7472 (m-30) REVERT: B 190 ARG cc_start: 0.7953 (tmm160) cc_final: 0.6644 (mtm180) REVERT: B 197 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8055 (pp20) REVERT: B 198 ASN cc_start: 0.8225 (t0) cc_final: 0.7867 (t0) REVERT: B 334 ARG cc_start: 0.7679 (ptp90) cc_final: 0.7336 (ttp80) REVERT: B 359 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5920 (mppt) REVERT: C 191 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 342 CYS cc_start: 0.8736 (t) cc_final: 0.7757 (p) REVERT: D 210 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: D 350 PHE cc_start: 0.7526 (m-80) cc_final: 0.7160 (m-80) REVERT: D 357 HIS cc_start: 0.6032 (m-70) cc_final: 0.5770 (m-70) REVERT: E 160 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4786 (tt0) REVERT: E 210 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: E 326 HIS cc_start: 0.8211 (t70) cc_final: 0.7977 (t-170) REVERT: E 342 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7561 (p) REVERT: E 380 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7049 (mtm-85) REVERT: F 160 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.4587 (tt0) REVERT: F 210 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: F 326 HIS cc_start: 0.8184 (t70) cc_final: 0.7841 (t-170) REVERT: F 380 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7662 (mtt180) REVERT: G 42 LEU cc_start: 0.1040 (OUTLIER) cc_final: 0.0799 (pp) REVERT: G 160 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.4217 (tt0) REVERT: G 210 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6366 (m-80) REVERT: G 326 HIS cc_start: 0.8349 (t70) cc_final: 0.8034 (t-170) outliers start: 93 outliers final: 72 residues processed: 287 average time/residue: 0.2815 time to fit residues: 128.7641 Evaluate side-chains 298 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 213 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 143 optimal weight: 0.0270 chunk 207 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 129 optimal weight: 0.0070 chunk 104 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** D 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.197849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132087 restraints weight = 27106.253| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.48 r_work: 0.3560 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20153 Z= 0.121 Angle : 0.645 11.585 27321 Z= 0.317 Chirality : 0.041 0.495 3122 Planarity : 0.005 0.062 3458 Dihedral : 5.600 58.871 2816 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.95 % Allowed : 29.37 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2394 helix: 1.88 (0.13), residues: 1645 sheet: -0.80 (0.60), residues: 105 loop : -2.50 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 115 HIS 0.003 0.000 HIS A 311 PHE 0.046 0.001 PHE E 350 TYR 0.017 0.001 TYR B 213 ARG 0.006 0.000 ARG G 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 7) link_NAG-ASN : angle 4.83907 ( 21) hydrogen bonds : bond 0.03161 ( 1244) hydrogen bonds : angle 4.08324 ( 3669) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.58085 ( 28) covalent geometry : bond 0.00266 (20132) covalent geometry : angle 0.63102 (27272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9327.92 seconds wall clock time: 162 minutes 12.40 seconds (9732.40 seconds total)